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    pdcd6ip programmed cell death 6 interacting protein [ Danio rerio (zebrafish) ]

    Gene ID: 406669, updated on 9-Dec-2024

    Summary

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    Official Symbol
    pdcd6ipprovided by ZNC
    Official Full Name
    programmed cell death 6 interacting proteinprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-2678
    See related
    Ensembl:ENSDARG00000025269 AllianceGenome:ZFIN:ZDB-GENE-040426-2678
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    zgc:63638; wu:fb70d03; wu:fy65h02
    Summary
    Predicted to be involved in mitotic cytokinesis. Predicted to act upstream of or within multivesicular body sorting pathway. Predicted to be active in endosome. Is expressed in cloaca; epidermis; otic vesicle; and sensory system. Human ortholog(s) of this gene implicated in primary autosomal recessive microcephaly. Orthologous to human PDCD6IP (programmed cell death 6 interacting protein). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See pdcd6ip in Genome Data Viewer
    Location:
    chromosome: 19
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 19 NC_007130.7 (42847305..42875185)
    105 previous assembly GRCz10 (GCF_000002035.5) 19 NC_007130.6 (43277837..43305748)

    Chromosome 19 - NC_007130.7Genomic Context describing neighboring genes Neighboring gene cytoplasmic linker associated protein 2 Neighboring gene upstream binding protein 1 Neighboring gene cAMP-regulated phosphoprotein, 21 Neighboring gene microRNA 128-2 Neighboring gene zinc finger TRAF-type containing 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Pathogenic copy number variants that affect gene expression contribute to genomic burden in cerebral palsy. Corbett MA, et al. NPJ Genom Med, 2018. PMID 30564460, Free PMC Article
    2. Zebrafish Melanoma-Derived Interstitial EVs Are Carriers of ncRNAs That Induce Inflammation. Biagini V, et al. Int J Mol Sci, 2022 May 14. PMID 35628321, Free PMC Article
    3. Common deregulated gene expression profiles and morphological changes in developing zebrafish larvae exposed to environmental-relevant high to low concentrations of glucocorticoids. Chen Q, et al. Chemosphere, 2017 Apr. PMID 28092764
    4. Crtap and p3h1 knock out zebrafish support defective collagen chaperoning as the cause of their osteogenesis imperfecta phenotype. Tonelli F, et al. Matrix Biol, 2020 Aug. PMID 32173581
    5. PI(3,4)P2-mediated cytokinetic abscission prevents early senescence and cataract formation. Gulluni F, et al. Science, 2021 Dec 10. PMID 34882480, Free PMC Article

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within multivesicular body sorting pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  

    General protein information

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    Preferred Names
    programmed cell death 6-interacting protein

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_213360.4 → NP_998525.2  programmed cell death 6-interacting protein

      Status: VALIDATED

      Source sequence(s)
      CU469582
      UniProtKB/TrEMBL
      A0A8N1Z4B2, B8JLR1, F1Q5T7
      Related
      ENSDARP00000121990.1, ENSDART00000135164.3
      Conserved Domains (4) summary
      cd09235
      Location:357 → 695
      V_Alix; Middle V-domain of mammalian Alix and related domains are dimerization and protein interaction modules
      cd09240
      Location:2 → 342
      BRO1_Alix; Protein-interacting, N-terminal, Bro1-like domain of mammalian Alix and related domains
      pfam13949
      Location:410 → 698
      ALIX_LYPXL_bnd; ALIX V-shaped domain binding to HIV
      cl23782
      Location:778 → 844
      RCR; Chitin synthesis regulation, resistance to Congo red

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007130.7 Reference GRCz11 Primary Assembly

      Range
      42847305..42875185
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005159737.5 → XP_005159794.1  programmed cell death 6-interacting protein isoform X1

      See identical proteins and their annotated locations for XP_005159794.1

      UniProtKB/TrEMBL
      A0A8M2B6D5
      Conserved Domains (4) summary
      cd09235
      Location:362 → 700
      V_Alix; Middle V-domain of mammalian Alix and related domains are dimerization and protein interaction modules
      cd09240
      Location:2 → 347
      BRO1_Alix; Protein-interacting, N-terminal, Bro1-like domain of mammalian Alix and related domains
      pfam13949
      Location:415 → 703
      ALIX_LYPXL_bnd; ALIX V-shaped domain binding to HIV
      cl23782
      Location:783 → 849
      RCR; Chitin synthesis regulation, resistance to Congo red

    2. XM_009294414.4 → XP_009292689.1  programmed cell death 6-interacting protein isoform X1

      See identical proteins and their annotated locations for XP_009292689.1

      UniProtKB/TrEMBL
      A0A8M2B6D5
      Conserved Domains (4) summary
      cd09235
      Location:362 → 700
      V_Alix; Middle V-domain of mammalian Alix and related domains are dimerization and protein interaction modules
      cd09240
      Location:2 → 347
      BRO1_Alix; Protein-interacting, N-terminal, Bro1-like domain of mammalian Alix and related domains
      pfam13949
      Location:415 → 703
      ALIX_LYPXL_bnd; ALIX V-shaped domain binding to HIV
      cl23782
      Location:783 → 849
      RCR; Chitin synthesis regulation, resistance to Congo red

    3. XM_068215110.1 → XP_068071211.1  programmed cell death 6-interacting protein isoform X2

      UniProtKB/TrEMBL
      A0A8N1Z4B2, B8JLR1, F1Q5T7
    Nucleotide Protein Strain
    Heading Accession and Version

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